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Feat: xyz file parsing - nAtoms & nLines to check formatting. Created… #52

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ac672c8
Feat: xyz file parsing - nAtoms & nLines to check formatting. Created…
adewyer Dec 30, 2021
c06358a
Feat: updates to move all functions for dealing w/ parsing xyz file a…
adewyer Jan 7, 2022
e5e38b6
simplified atomsCount function for xyz file and updated function name…
adewyer Jan 7, 2022
aef4e7b
removed unused function from parsers
adewyer Jan 7, 2022
65c6528
updated tests for new function naming
adewyer Jan 7, 2022
6ef320c
moved functions and updated naming based on PR comments
adewyer Jan 8, 2022
78572e9
moved defaultMaterialConfig to it's own file to avoid circular imports
adewyer Jan 13, 2022
df31214
feat: git lfs pull
tjduigna Jan 13, 2022
bce5e1b
remove eslint-disable-next-line import/no-cycle
adewyer Jan 13, 2022
2877ebc
Merge branch 'feature/SOF-5388' of github.com:Exabyte-io/made-js into…
adewyer Jan 13, 2022
d859afc
updated functions for converting between formats
adewyer Feb 12, 2022
8750dae
updated how we copy the default material in converting other formats …
adewyer Feb 16, 2022
431a269
updates for converting xyz --> poscar without altering default material
adewyer Feb 16, 2022
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16 changes: 16 additions & 0 deletions src/parsers/xyz.js
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
import Integer from "lodash/string";
import _ from "underscore";
import s from "underscore.string";

Expand Down Expand Up @@ -140,10 +141,25 @@ function fromMaterial(materialOrConfig, fractional = false) {
return fromBasis(basis, "%11.6f");
}

export function atomsCount(xyzFile) {
const xyzArray = xyzFile.split(/\r?\n/);
return Integer.parseInt(xyzArray[0]);

@timurbazhirov timurbazhirov Jan 6, 2022

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  1. Why do we even need this function, if all this does is just split on newlines? This is not specific to XYZ format, is it?
  2. No docstring, explanation of the expected behavior

@adewyer adewyer Jan 7, 2022

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The first line of an xyz file contains the number of atoms. So we split the string by new lines and then return the first new line to get the number of atoms in the file.

}

export function linesCount(xyzFile) {
const content = xyzFile.split(/\r?\n/);
if (!content[-1]) {
content.pop();
}

@timurbazhirov timurbazhirov Jan 6, 2022

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Not sure what's happening above - no explanation either.

return content.length;
}

export default {
validate,
fromMaterial,
toBasisConfig,
fromBasis,
CombinatorialBasis,
atomsCount,
linesCount,
};
2 changes: 2 additions & 0 deletions tests/enums.js
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Expand Up @@ -31,3 +31,5 @@ export const SiPWSCFInput = readFile(path.join(FIXTURES_DIR, "Si-pwscf.in"));
export const Zr1H23Zr1H1 = readJSONFile(path.join(FIXTURES_DIR, "Zr1H23Zr1H1.json"));
export const Zr1H23Zr1H1Poscar = readFile(path.join(FIXTURES_DIR, "Zr1H23Zr1H1.poscar"));
export const H2O = readFile(path.join(FIXTURES_DIR, "H2O.poscar"));

export const CH4 = readFile(path.join(FIXTURES_DIR, "CH4.xyz"));
3 changes: 3 additions & 0 deletions tests/fixtures/CH4.xyz
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11 changes: 10 additions & 1 deletion tests/parsers/xyz.js
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Original file line number Diff line number Diff line change
@@ -1,5 +1,8 @@
import { expect } from "chai";

import parsers from "../../src/parsers/parsers";
import { Si } from "../enums";
import { atomsCount, linesCount } from "../../src/parsers/xyz";
import { CH4, Si } from "../enums";
import { assertDeepAlmostEqual } from "../utils";

describe("Parsers:XYZ", () => {
Expand All @@ -11,4 +14,10 @@ describe("Parsers:XYZ", () => {
"units",
]);
});
it("should return the number of atoms for a molecule in an xyz file", () => {
expect(atomsCount(CH4)).to.be.equal(5);
});
it("should return the number of lines in an xyz file", () => {
expect(linesCount(CH4)).to.be.equal(7);
});
});